First stage of string modernisation

MDANSE/Src/MDANSE/Chemistry/Databases.py

@@ -480,18 +480,19 @@ def info(self, atom: str) -> str:
 
         # A delimiter line.
         delimiter = "-" * 70
+        tab_fmt = "{:<20}{:>50}"
 
         info = [
             delimiter,
-            "%s" % atom.center(70),
-            "%s" % " {0:<20}{1:>50}".format("property", "value"),
+            f"{atom:^70}",
+            tab_fmt.format("property", "value"),
             delimiter,
         ]
 
         # The values for all element's properties
         for pname in sorted(self._properties):
             info.append(
-                " {0:<20}{1:>50}".format(pname, str(self._data[atom].get(pname, None)))
+                tab_fmt.format(pname, self._data[atom].get(pname, None))
             )
 
         info.append(delimiter)

MDANSE/Src/MDANSE/Framework/Configurable.py

@@ -31,14 +31,14 @@ class ConfigurationError(Error):
 class Configurable(object):
     """
     This class allows any object that derives from it to be configurable within the MDANSE framework.
-    
+
     Within that framework, to be configurable, a class must:
         #. derive from this class
         #. implement the "configurators"  class attribute as a list of 3-tuple whose:
             #.. 0-value is the type of the configurator that will be used to fetch the corresponding \
             MDANSE.Framework.Configurators.IConfigurator.IConfigurator derived class from the configurators registry
             #.. 1-value is the name of the configurator that will be used as the key of the _configuration attribute.
-            #.. 2-value is the dictionary of the keywords used when initializing the configurator.  
+            #.. 2-value is the dictionary of the keywords used when initializing the configurator.
     """
 
     enabled = True
@@ -94,7 +94,7 @@ def build_configuration(self):
                 )
             # Any kind of error has to be caught
             except:
-                raise ConfigurationError("Could not set %r configuration item" % name)
+                raise ConfigurationError(f"Could not set {name!r} configuration item")
 
     def set_settings(self, settings):
         self.settings = settings
@@ -228,10 +228,10 @@ def build_doc_example(cls):
         docstring += ">>> \n"
         docstring += ">>> \n"
         docstring += ">>> parameters = {}\n"
-        for k, v in list(cls.get_default_parameters().items()):
-            docstring += ">>> parameters[%r]=%r\n" % (k, v)
+        for k, v in cls.get_default_parameters().items():
+            docstring += f">>> parameters[{k!r}]={v!r}\n"
         docstring += ">>> \n"
-        docstring += ">>> job = IJob.create(%r)\n" % cls.__name__
+        docstring += f">>> job = IJob.create({cls.__name__!r})\n"
         docstring += ">>> job.setup(parameters)\n"
         docstring += ">>> job.run()\n"
         return docstring
@@ -249,53 +249,23 @@ def build_doc_texttable(cls, doclist):
             sizes[1] = max(sizes[1], len(v["Default value"]))
             # Case of Description field: has to be splitted and parsed for inserting sphinx "|" keyword for multiline
             v["Description"] = v["Description"].strip()
-            v["Description"] = v["Description"].split("\n")
+            v["Description"] = v["Description"].splitlines()
             v["Description"] = ["| " + vv.strip() for vv in v["Description"]]
-            sizes[2] = max(sizes[2], max([len(d) for d in v["Description"]]))
-
-        docstring += "+%s+%s+%s+\n" % (
-            "-" * (sizes[0] + 1),
-            "-" * (sizes[1] + 1),
-            "-" * (sizes[2] + 1),
-        )
-        docstring += "| %-*s| %-*s| %-*s|\n" % (
-            sizes[0],
-            columns[0],
-            sizes[1],
-            columns[1],
-            sizes[2],
-            columns[2],
-        )
-        docstring += "+%s+%s+%s+\n" % (
-            "=" * (sizes[0] + 1),
-            "=" * (sizes[1] + 1),
-            "=" * (sizes[2] + 1),
-        )
+            sizes[2] = max(sizes[2], max(v["Description"], key=len))
+
+        data_line = "| " + "| ".join(f"{{}}:<{size}" for size in sizes) + "|\n"
+        sep_line = "+" + "+".join("-" * (size+1) for size in sizes) + "+\n"
+
+        docstring += sep_line
+        docstring += data_line.format(*columns)
+        docstring += sep_line.replace("-", "=")
 
         for v in doclist:
-            docstring += "| %-*s| %-*s| %-*s|\n" % (
-                sizes[0],
-                v["Configurator"],
-                sizes[1],
-                v["Default value"],
-                sizes[2],
-                v["Description"][0],
-            )
+            docstring += data_line.format(v["Configurator"], v["Default value"], v["Description"][0])
             if len(v["Description"]) > 1:
                 for descr in v["Description"][1:]:
-                    docstring += "| %-*s| %-*s| %-*s|\n" % (
-                        sizes[0],
-                        "",
-                        sizes[1],
-                        "",
-                        sizes[2],
-                        descr,
-                    )
-            docstring += "+%s+%s+%s+\n" % (
-                "-" * (sizes[0] + 1),
-                "-" * (sizes[1] + 1),
-                "-" * (sizes[2] + 1),
-            )
+                    data_line.format("", "", descr)
+            docstring += sep_line
 
         docstring += "\n"
         return docstring

MDANSE/Src/MDANSE/Framework/Configurators/AseInputFileConfigurator.py

@@ -105,4 +105,4 @@ def get_information(self):
             LOG.error(result)
             return result
         else:
-            return "Input file: %r\n" % self["value"]
+            return f"Input file: {self['value']!r}\n"

MDANSE/Src/MDANSE/Framework/Configurators/AtomSelectionConfigurator.py

@@ -127,8 +127,8 @@ def get_information(self) -> str:
             return "Not configured yet\n"
 
         info = []
-        info.append("Number of selected atoms:%d" % self["selection_length"])
-        info.append("Selected elements:%s" % self["unique_names"])
+        info.append(f"Number of selected atoms:{self['selection_length']:d}")
+        info.append(f"Selected elements:{self['unique_names']}")
 
         return "\n".join(info) + "\n"
 

MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py

@@ -203,7 +203,7 @@ def get_information(self) -> str:
         if self["value"] is None:
             return "No atoms selected for transmutation\n"
 
-        return "Number of transmuted atoms:%d\n" % self._nTransmutedAtoms
+        return f"Number of transmuted atoms:{self._nTransmutedAtoms:d}\n"
 
     def get_transmuter(self) -> AtomTransmuter:
         """

MDANSE/Src/MDANSE/Framework/Configurators/AtomsListConfigurator.py

@@ -64,10 +64,10 @@ def configure(self, value):
         traj_configurator = self._configurable[self._dependencies["trajectory"]]
 
         if UD_STORE.has_definition(
-            traj_configurator["basename"], "%d_atoms_list" % self._nAtoms, value
+            traj_configurator["basename"], f"{self._nAtoms:d}_atoms_list", value
         ):
             molecule, atoms = UD_STORE.get_definition(
-                traj_configurator["basename"], "%d_atoms_list" % self._nAtoms, value
+                traj_configurator["basename"], f"{self._nAtoms:d}_atoms_list", value
             )
         elif UD_STORE.has_definition(
             traj_configurator["basename"], "AtomsListConfigurator", value
@@ -78,11 +78,8 @@ def configure(self, value):
             natoms = tempdict["natoms"]
             if not natoms == self._nAtoms:
                 raise ValueError(
-                    "The atom list must have "
-                    + str(self._nAtoms)
-                    + " atoms per molecule, but "
-                    + str(natoms)
-                    + " were found."
+                    f"The atom list must have {self._nAtoms} "
+                    f"atoms per molecule, but {natoms} were found."
                 )
             atoms = tempdict["indices"]
             self["value"] = value
@@ -111,9 +108,6 @@ def get_information(self):
         if "atoms" not in self:
             return "No configured yet"
 
-        info = []
-        info.append(
-            "Number of selected %d-tuplets:%d" % (self._nAtoms, self["n_values"])
-        )
+        info = [f"Number of selected {self._nAtoms:d}-tuplets:{self['n_values']:d}"]
 
         return "\n".join(info) + "\n"

MDANSE/Src/MDANSE/Framework/Configurators/AxisSelectionConfigurator.py

@@ -33,19 +33,19 @@ class AxisSelectionConfigurator(IConfigurator):
 
     def configure(self, value):
         """
-        Configure an input value. 
-        
+        Configure an input value.
+
         The value can be:
-        
+
         #. a dict with *'molecule'*, *'endpoint1'* and *'endpoint2'* keys. *'molecule'* key \
         is the name of the molecule for which the axis selection will be performed and *'endpoint1'* \
-        and *'endpoint2'* keys are the names of two atoms of the molecule along which the axis will be defined  
+        and *'endpoint2'* keys are the names of two atoms of the molecule along which the axis will be defined
         #. str: the axis selection will be performed by reading the corresponding user definition.
-        
+
         :param configuration: the current configuration
         :type configuration: MDANSE.Framework.Configurable.Configurable
         :param value: the input value
-        :type value: tuple or str 
+        :type value: tuple or str
         """
         self._original_input = value
 
@@ -88,4 +88,4 @@ def get_information(self):
         if "value" not in self:
             return "Not configured yet\n"
 
-        return "Axis vector:%s\n" % self["value"]
+        return f"Axis vector:{self['value']}\n"

MDANSE/Src/MDANSE/Framework/Configurators/BasisSelectionConfigurator.py

@@ -33,17 +33,17 @@ class BasisSelectionConfigurator(IConfigurator):
 
     def configure(self, value):
         """
-        Configure an input value. 
-        
+        Configure an input value.
+
         The value can be:
-        
+
         #. a dict with *'molecule'*, *'origin'*, *'x_axis'* and *'y_axis'* keys. *'molecule'* key is \
         the name of the molecule for which the axis selection will be performed and *'origin'*, *'x_axis'* and *'y_axis'* \
-        keys are the names of three atoms of the molecule that will be used to define respectively the origin, the X and Y axis of the basis  
+        keys are the names of three atoms of the molecule that will be used to define respectively the origin, the X and Y axis of the basis
         #. str: the axis selection will be performed by reading the corresponding user definition.
-        
+
         :param value: the input value
-        :type value: tuple or str 
+        :type value: tuple or str
 
         :note: this configurator depends on 'trajectory' configurator to be configured
         """
@@ -85,4 +85,4 @@ def get_information(self):
         if "value" not in self:
             return "Not configured yet\n"
 
-        return "Basis vector:%s\n" % self["value"]
+        return f"Basis vector:{self['value']}\n"

MDANSE/Src/MDANSE/Framework/Configurators/BooleanConfigurator.py

@@ -70,4 +70,4 @@ def get_information(self):
         if "value" not in self:
             return "Not configured yet\n"
 
-        return "Value: %r\n" % self["value"]
+        return f"Value: {self['value']!r}\n"

MDANSE/Src/MDANSE/Framework/Configurators/FloatConfigurator.py

@@ -125,4 +125,4 @@ def get_information(self):
         if "value" not in self:
             return "Not configured yet\n"
 
-        return "Value: %r\n" % self["value"]
+        return f"Value: {self['value']!r}\n"

MDANSE/Src/MDANSE/Framework/Configurators/FramesConfigurator.py

@@ -19,9 +19,9 @@
 class FramesConfigurator(RangeConfigurator):
     """
     This configurator allows to input a frame selection for the analysis.
-    
+
     The frame selection can be input as:
-    
+
     #. a 3-tuple where the 1st, 2nd will correspond respectively to the indices of the first and \
     last (excluded) frames to be selected while the 3rd element will correspond to the step number between two frames. For example (1,11,3) will give 1,4,7,10
     #. *'all'* keyword, in such case, all the frames of the trajectory are selected
@@ -123,13 +123,8 @@ def get_information(self):
 
         try:
             result = (
-                "%d frames selected (first=%.3f ; last = %.3f ; time step = %.3f)\n"
-                % (
-                    self["n_frames"],
-                    self["time"][0],
-                    self["time"][-1],
-                    self["time_step"],
-                )
+                f"{self['n_frames']} frames selected "
+                f"(first={self['time'][0]:.3f} ; last = {self['time'][-1]:.3f} ; time step = {self['time_step']:.3f})\n"
             )
         except KeyError:
             result = "FramesConfigurator could not be configured!"

MDANSE/Src/MDANSE/Framework/Configurators/GroupingLevelConfigurator.py

@@ -149,4 +149,4 @@ def get_information(self):
         if "value" not in self:
             return "Not configured yet\n"
 
-        return "Grouping level: %r\n" % self["value"]
+        return f"Grouping level: {self['value']!r}\n"

MDANSE/Src/MDANSE/Framework/Configurators/HDFInputFileConfigurator.py

@@ -117,14 +117,14 @@ def get_information(self):
         if "value" not in self:
             return "Not configured yet\n"
 
-        info = ["HDF input file: %r" % self["value"]]
+        info = [f"HDF input file: {self['value']!r}"]
 
         if "instance" in self:
             info.append("Contains the following variables:")
             variables = []
             find_numeric_variables(variables, self["instance"])
 
             for v in variables:
-                info.append("\t-{}".format(v))
+                info.append(f"\t-{v}")
 
         return "\n".join(info) + "\n"

MDANSE/Src/MDANSE/Framework/Configurators/HDFTrajectoryConfigurator.py

@@ -80,14 +80,13 @@ def get_information(self):
         :rtype: str
         """
         try:
-            info = ["HDF input trajectory: %r\n" % self["filename"]]
-            info.append("Number of steps: %d\n" % self["length"])
+            info = [f"HDF input trajectory: {self['filename']!r}\n"]
+            info.append(f"Number of steps: {self['length']:d}\n")
         except KeyError:
             info = "Input trajectory has not been configured"
         else:
             info.append(
-                "Size of the chemical system: %d\n"
-                % self["instance"].chemical_system.number_of_atoms
+                f"Size of the chemical system: {self['instance'].chemical_system.number_of_atoms:d}\n"
             )
 
             if self["has_velocities"]:

MDANSE/Src/MDANSE/Framework/Configurators/IConfigurator.py

@@ -59,10 +59,7 @@ def __str__(self):
         """
 
         if self._configurator is not None:
-            self._message = "Configurator: %r --> %s" % (
-                self._configurator.name,
-                self._message,
-            )
+            self._message = f"Configurator: {self._configurator.name!r} --> {self._message}"
 
         return self._message
 

MDANSE/Src/MDANSE/Framework/Configurators/InputDirectoryConfigurator.py

@@ -56,4 +56,4 @@ def get_information(self):
         if "value" not in self:
             return "Not configured yet\n"
 
-        return "Input directory: %r\n" % self["value"]
+        return f"Input directory: {self['value']!r}\n"

MDANSE/Src/MDANSE/Framework/Configurators/InstrumentResolutionConfigurator.py

@@ -53,7 +53,7 @@ class InstrumentResolutionConfigurator(IConfigurator):
     def configure(self, value):
         """
         Configure the instrument resolution.
-                
+
         :param value: the instrument resolution. It must a 2-tuple where the 1st element is the \
         is a string representing one of the supported instrument resolution and the 2nd element \
         is a dictionary that stores the parameters for this kernel.
@@ -122,11 +122,11 @@ def get_information(self):
         if "kernel" not in self:
             return "No configured yet"
 
-        info = ["Instrument resolution kernel: %s" % self["kernel"]]
+        info = [f"Instrument resolution kernel: {self['kernel']}"]
         if self["parameters"]:
             info.append("Parameters:")
-            for k, v in list(self["parameters"].items()):
-                info.append("%s = %s" % (k, v))
+            for k, v in self["parameters"].items():
+                info.append(f"{k} = {v}")
 
         info = "\n".join(info)
 

MDANSE/Src/MDANSE/Framework/Configurators/IntegerConfigurator.py

@@ -137,4 +137,4 @@ def get_information(self):
         if "value" not in self:
             return "Not configured yet\n"
 
-        return "Value: %r\n" % self["value"]
+        return f"Value: {self['value']!r}\n"

MDANSE/Src/MDANSE/Framework/Configurators/MDMCTrajectoryConfigurator.py

@@ -72,10 +72,9 @@ def get_information(self):
         """
 
         info = ["MDMC trajectory used as input"]
-        info.append("Number of steps: %d\n" % self["length"])
+        info.append(f"Number of steps: {self['length']:d}\n")
         info.append(
-            "Size of the chemical system: %d\n"
-            % self["instance"].chemical_system.number_of_atoms
+            f"Size of the chemical system: {self['instance'].chemical_system.number_of_atoms:d}\n"
         )
         if self["has_velocities"]:
             info.append("The trajectory contains atomic velocities\n")